src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.GroupUrlLink;
  34 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  35 import jalview.util.UrlLink;
  36
  37 /**
  38  * DOCUMENT ME!
  39  *
  40  * @author $author$
  41  * @version $Revision: 1.118 $
  42  */
  43 public class PopupMenu extends JPopupMenu
  44 {
  45   JMenu groupMenu = new JMenu();
  46
  47   JMenuItem groupName = new JMenuItem();
  48
  49   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  62
  63   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  64
  65   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  66
  67   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  70
  71   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  72
  73   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  74
  75   //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem();
  76
  77   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  78
  79   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  80
  81   AlignmentPanel ap;
  82
  83   JMenu sequenceMenu = new JMenu();
  84
  85   JMenuItem sequenceName = new JMenuItem();
  86
  87   Sequence sequence;
  88
  89   JMenuItem unGroupMenuItem = new JMenuItem();
  90
  91   JMenuItem outline = new JMenuItem();
  92
  93   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  94
  95   JMenu colourMenu = new JMenu();
  96
  97   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  98
  99   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 100
 101   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 102
 103   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 104
 105   JMenu editMenu = new JMenu();
 106
 107   JMenuItem cut = new JMenuItem();
 108
 109   JMenuItem copy = new JMenuItem();
 110
 111   JMenuItem upperCase = new JMenuItem();
 112
 113   JMenuItem lowerCase = new JMenuItem();
 114
 115   JMenuItem toggle = new JMenuItem();
 116
 117   JMenu pdbMenu = new JMenu();
 118
 119   JMenuItem pdbFromFile = new JMenuItem();
 120
 121   JMenuItem enterPDB = new JMenuItem();
 122
 123   JMenuItem discoverPDB = new JMenuItem();
 124
 125   JMenu outputMenu = new JMenu();
 126
 127   JMenuItem sequenceFeature = new JMenuItem();
 128
 129   JMenuItem textColour = new JMenuItem();
 130
 131   JMenu jMenu1 = new JMenu();
 132
 133   JMenu structureMenu = new JMenu();
 134
 135   JMenu viewStructureMenu = new JMenu();
 136
 137   // JMenu colStructureMenu = new JMenu();
 138   JMenuItem editSequence = new JMenuItem();
 139
 140   // JMenuItem annotationMenuItem = new JMenuItem();
 141
 142   JMenu groupLinksMenu;
 143
 144   /**
 145    * Creates a new PopupMenu object.
 146    *
 147    * @param ap
 148    *          DOCUMENT ME!
 149    * @param seq
 150    *          DOCUMENT ME!
 151    */
 152   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 153   {
 154     this(ap, seq, links, null);
 155   }
 156
 157   /**
 158    *
 159    * @param ap
 160    * @param seq
 161    * @param links
 162    * @param groupLinks
 163    */
 164   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
 165           Vector groupLinks)
 166   {
 167     // /////////////////////////////////////////////////////////
 168     // If this is activated from the sequence panel, the user may want to
 169     // edit or annotate a particular residue. Therefore display the residue menu
 170     //
 171     // If from the IDPanel, we must display the sequence menu
 172     // ////////////////////////////////////////////////////////
 173     this.ap = ap;
 174     sequence = seq;
 175
 176     ButtonGroup colours = new ButtonGroup();
 177     colours.add(noColourmenuItem);
 178     colours.add(clustalColour);
 179     colours.add(zappoColour);
 180     colours.add(taylorColour);
 181     colours.add(hydrophobicityColour);
 182     colours.add(helixColour);
 183     colours.add(strandColour);
 184     colours.add(turnColour);
 185     colours.add(buriedColour);
 186     colours.add(abovePIDColour);
 187     colours.add(userDefinedColour);
 188     colours.add(PIDColour);
 189     colours.add(BLOSUM62Colour);
 190     colours.add(purinePyrimidineColour);
 191     //colours.add(covariationColour);
 192
 193     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 194     {
 195       JMenuItem item = new JMenuItem(
 196               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 197
 198       item.addActionListener(new java.awt.event.ActionListener()
 199       {
 200         public void actionPerformed(ActionEvent e)
 201         {
 202           outputText_actionPerformed(e);
 203         }
 204       });
 205
 206       outputMenu.add(item);
 207     }
 208
 209     try
 210     {
 211       jbInit();
 212     } catch (Exception e)
 213     {
 214       e.printStackTrace();
 215     }
 216
 217     if (seq != null)
 218     {
 219       sequenceMenu.setText(sequence.getName());
 220
 221       JMenuItem menuItem;
 222       if (seq.getDatasetSequence().getPDBId() != null
 223               && seq.getDatasetSequence().getPDBId().size() > 0)
 224       {
 225         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 226                 .elements();
 227
 228         while (e.hasMoreElements())
 229         {
 230           final PDBEntry pdb = (PDBEntry) e.nextElement();
 231
 232           menuItem = new JMenuItem();
 233           menuItem.setText(pdb.getId());
 234           menuItem.addActionListener(new java.awt.event.ActionListener()
 235           {
 236             public void actionPerformed(ActionEvent e)
 237             {
 238                 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
 239               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
 240               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 241             }
 242
 243           });
 244           viewStructureMenu.add(menuItem);
 245
 246           /*
 247            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 248            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 249            * public void actionPerformed(ActionEvent e) {
 250            * colourByStructure(pdb.getId()); } });
 251            * colStructureMenu.add(menuItem);
 252            */
 253         }
 254       }
 255       else
 256       {
 257         //JAN structureMenu.remove(viewStructureMenu);
 258         // structureMenu.remove(colStructureMenu);
 259       }
 260
 261       //if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S'){
 262       //TODO: Something to check if it's an RNA
 263           //like: if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S')
 264           final SequenceI seqI = seq.getDatasetSequence();
 265           //ap.getAlignment().get
 266           menuItem = new JMenuItem();
 267           menuItem.setText("RNA structure");
 268       menuItem.addActionListener(new java.awt.event.ActionListener()
 269       {
 270         public void actionPerformed(ActionEvent e)
 271         {
 272                 System.out.println("Call Varna "+seqI.getSequenceAsString()+" "+seqI.getName());
 273                 new AppVarna(seqI.getSequenceAsString(),seqI.getName());
 274
 275         }
 276       });
 277       viewStructureMenu.add(menuItem);
 278       //}
 279
 280
 281       menuItem = new JMenuItem("Hide Sequences");
 282       menuItem.addActionListener(new java.awt.event.ActionListener()
 283       {
 284         public void actionPerformed(ActionEvent e)
 285         {
 286           hideSequences(false);
 287         }
 288       });
 289       add(menuItem);
 290
 291       if (ap.av.getSelectionGroup() != null
 292               && ap.av.getSelectionGroup().getSize() > 1)
 293       {
 294         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 295         menuItem.addActionListener(new java.awt.event.ActionListener()
 296         {
 297           public void actionPerformed(ActionEvent e)
 298           {
 299             hideSequences(true);
 300           }
 301         });
 302         sequenceMenu.add(menuItem);
 303       }
 304
 305       if (ap.av.hasHiddenRows)
 306       {
 307         final int index = ap.av.alignment.findIndex(seq);
 308
 309         if (ap.av.adjustForHiddenSeqs(index)
 310                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 311         {
 312           menuItem = new JMenuItem("Reveal Sequences");
 313           menuItem.addActionListener(new ActionListener()
 314           {
 315             public void actionPerformed(ActionEvent e)
 316             {
 317               ap.av.showSequence(index);
 318               if (ap.overviewPanel != null)
 319               {
 320                 ap.overviewPanel.updateOverviewImage();
 321               }
 322             }
 323           });
 324           add(menuItem);
 325         }
 326
 327         menuItem = new JMenuItem("Reveal All");
 328         menuItem.addActionListener(new ActionListener()
 329         {
 330           public void actionPerformed(ActionEvent e)
 331           {
 332             ap.av.showAllHiddenSeqs();
 333             if (ap.overviewPanel != null)
 334             {
 335               ap.overviewPanel.updateOverviewImage();
 336             }
 337           }
 338         });
 339
 340         add(menuItem);
 341       }
 342
 343     }
 344
 345     SequenceGroup sg = ap.av.getSelectionGroup();
 346
 347     if (sg != null)
 348     {
 349       groupName.setText("Name: "+sg.getName());
 350       groupName.setText("Edit name and description of current group.");
 351
 352       if (sg.cs instanceof ZappoColourScheme)
 353       {
 354         zappoColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof TaylorColourScheme)
 357       {
 358         taylorColour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof PIDColourScheme)
 361       {
 362         PIDColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof Blosum62ColourScheme)
 365       {
 366         BLOSUM62Colour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof UserColourScheme)
 369       {
 370         userDefinedColour.setSelected(true);
 371       }
 372       else if (sg.cs instanceof HydrophobicColourScheme)
 373       {
 374         hydrophobicityColour.setSelected(true);
 375       }
 376       else if (sg.cs instanceof HelixColourScheme)
 377       {
 378         helixColour.setSelected(true);
 379       }
 380       else if (sg.cs instanceof StrandColourScheme)
 381       {
 382         strandColour.setSelected(true);
 383       }
 384       else if (sg.cs instanceof TurnColourScheme)
 385       {
 386         turnColour.setSelected(true);
 387       }
 388       else if (sg.cs instanceof BuriedColourScheme)
 389       {
 390         buriedColour.setSelected(true);
 391       }
 392       else if (sg.cs instanceof ClustalxColourScheme)
 393       {
 394         clustalColour.setSelected(true);
 395       }
 396       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 397       {
 398         purinePyrimidineColour.setSelected(true);
 399       }
 400      /* else if (sg.cs instanceof CovariationColourScheme)
 401       {
 402         covariationColour.setSelected(true);
 403       }*/
 404       else
 405       {
 406         noColourmenuItem.setSelected(true);
 407       }
 408
 409       if (sg.cs != null && sg.cs.conservationApplied())
 410       {
 411         conservationMenuItem.setSelected(true);
 412       }
 413       displayNonconserved.setSelected(sg.getShowNonconserved());
 414       showText.setSelected(sg.getDisplayText());
 415       showColourText.setSelected(sg.getColourText());
 416       showBoxes.setSelected(sg.getDisplayBoxes());
 417       // add any groupURLs to the groupURL submenu and make it visible
 418       if (groupLinks != null && groupLinks.size() > 0)
 419       {
 420         buildGroupURLMenu(sg, groupLinks);
 421       }
 422       // Add a 'show all structures' for the current selection
 423       Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
 424       for (SequenceI sq: ap.av.getSequenceSelection())
 425       {
 426         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
 427         if (pes!=null) {
 428           for (PDBEntry pe: pes)
 429           {
 430             pdbe.put(pe.getId(),  pe);
 431           }
 432         }
 433       }
 434       if (pdbe.size()>0)
 435       {
 436         final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
 437         final JMenuItem gpdbview;
 438         structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
 439         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 440         gpdbview.addActionListener(new ActionListener()
 441         {
 442
 443           @Override
 444           public void actionPerformed(ActionEvent e)
 445           {
 446             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 447           }
 448         });
 449       }
 450     }
 451     else
 452     {
 453       groupMenu.setVisible(false);
 454       editMenu.setVisible(false);
 455     }
 456
 457     if (!ap.av.alignment.getGroups().contains(sg))
 458     {
 459       unGroupMenuItem.setVisible(false);
 460     }
 461
 462     if (seq == null)
 463     {
 464       sequenceMenu.setVisible(false);
 465       structureMenu.setVisible(false);
 466     }
 467
 468     if (links != null && links.size() > 0)
 469     {
 470
 471       JMenu linkMenu = new JMenu("Link");
 472       Vector linkset = new Vector();
 473       for (int i = 0; i < links.size(); i++)
 474       {
 475         String link = links.elementAt(i).toString();
 476         UrlLink urlLink = null;
 477         try
 478         {
 479           urlLink = new UrlLink(link);
 480         } catch (Exception foo)
 481         {
 482           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 483                   + "'", foo);
 484           continue;
 485         }
 486         ;
 487         if (!urlLink.isValid())
 488         {
 489           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 490           continue;
 491         }
 492         final String label = urlLink.getLabel();
 493         if (urlLink.isDynamic())
 494         {
 495
 496           // collect matching db-refs
 497           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 498                   seq.getDBRef(), new String[]
 499                   { urlLink.getTarget() });
 500           // collect id string too
 501           String id = seq.getName();
 502           String descr = seq.getDescription();
 503           if (descr != null && descr.length() < 1)
 504           {
 505             descr = null;
 506           }
 507
 508           if (dbr != null)
 509           {
 510             for (int r = 0; r < dbr.length; r++)
 511             {
 512               if (id != null && dbr[r].getAccessionId().equals(id))
 513               {
 514                 // suppress duplicate link creation for the bare sequence ID
 515                 // string with this link
 516                 id = null;
 517               }
 518               // create Bare ID link for this RUL
 519               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 520                       true);
 521               if (urls != null)
 522               {
 523                 for (int u = 0; u < urls.length; u += 2)
 524                 {
 525                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 526                   {
 527                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 528                     addshowLink(linkMenu, label + "|" + urls[u],
 529                             urls[u + 1]);
 530                   }
 531                 }
 532               }
 533             }
 534           }
 535           if (id != null)
 536           {
 537             // create Bare ID link for this RUL
 538             String[] urls = urlLink.makeUrls(id, true);
 539             if (urls != null)
 540             {
 541               for (int u = 0; u < urls.length; u += 2)
 542               {
 543                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 544                 {
 545                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 546                   addshowLink(linkMenu, label, urls[u + 1]);
 547                 }
 548               }
 549             }
 550           }
 551           // Create urls from description but only for URL links which are regex
 552           // links
 553           if (descr != null && urlLink.getRegexReplace() != null)
 554           {
 555             // create link for this URL from description where regex matches
 556             String[] urls = urlLink.makeUrls(descr, true);
 557             if (urls != null)
 558             {
 559               for (int u = 0; u < urls.length; u += 2)
 560               {
 561                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 562                 {
 563                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 564                   addshowLink(linkMenu, label, urls[u + 1]);
 565                 }
 566               }
 567             }
 568           }
 569         }
 570         else
 571         {
 572           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 573           {
 574             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 575             // Add a non-dynamic link
 576             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 577           }
 578         }
 579       }
 580       if (sequence != null)
 581       {
 582         sequenceMenu.add(linkMenu);
 583       }
 584       else
 585       {
 586         add(linkMenu);
 587       }
 588     }
 589   }
 590
 591   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 592   {
 593
 594     // TODO: usability: thread off the generation of group url content so root
 595     // menu appears asap
 596     // sequence only URLs
 597     // ID/regex match URLs
 598     groupLinksMenu = new JMenu("Group Link");
 599     JMenu[] linkMenus = new JMenu[]
 600     { null, new JMenu("IDS"), new JMenu("Sequences"),
 601         new JMenu("IDS and Sequences") }; // three types of url that might be
 602                                           // created.
 603     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 604     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 605     Hashtable commonDbrefs = new Hashtable();
 606     for (int sq = 0; sq < seqs.length; sq++)
 607     {
 608
 609       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 610               .findPosition(sg.getEndRes());
 611       // just collect ids from dataset sequence
 612       // TODO: check if IDs collected from selecton group intersects with the
 613       // current selection, too
 614       SequenceI sqi = seqs[sq];
 615       while (sqi.getDatasetSequence() != null)
 616       {
 617         sqi = sqi.getDatasetSequence();
 618       }
 619       DBRefEntry[] dbr = sqi.getDBRef();
 620       if (dbr != null && dbr.length > 0)
 621       {
 622         for (int d = 0; d < dbr.length; d++)
 623         {
 624           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 625           Object[] sarray = (Object[]) commonDbrefs.get(src);
 626           if (sarray == null)
 627           {
 628             sarray = new Object[2];
 629             sarray[0] = new int[]
 630             { 0 };
 631             sarray[1] = new String[seqs.length];
 632
 633             commonDbrefs.put(src, sarray);
 634           }
 635
 636           if (((String[]) sarray[1])[sq] == null)
 637           {
 638             if (!dbr[d].hasMap()
 639                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 640             {
 641               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 642               ((int[]) sarray[0])[0]++;
 643             }
 644           }
 645         }
 646       }
 647     }
 648     // now create group links for all distinct ID/sequence sets.
 649     boolean addMenu = false; // indicates if there are any group links to give
 650                              // to user
 651     for (int i = 0; i < groupLinks.size(); i++)
 652     {
 653       String link = groupLinks.elementAt(i).toString();
 654       GroupUrlLink urlLink = null;
 655       try
 656       {
 657         urlLink = new GroupUrlLink(link);
 658       } catch (Exception foo)
 659       {
 660         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 661                 + "'", foo);
 662         continue;
 663       }
 664       ;
 665       if (!urlLink.isValid())
 666       {
 667         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 668         continue;
 669       }
 670       final String label = urlLink.getLabel();
 671       boolean usingNames = false;
 672       // Now see which parts of the group apply for this URL
 673       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 674       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 675       String[] seqstr, ids; // input to makeUrl
 676       if (idset != null)
 677       {
 678         int numinput = ((int[]) idset[0])[0];
 679         String[] allids = ((String[]) idset[1]);
 680         seqstr = new String[numinput];
 681         ids = new String[numinput];
 682         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 683         {
 684           if (allids[sq] != null)
 685           {
 686             ids[idcount] = allids[sq];
 687             seqstr[idcount++] = idandseqs[1][sq];
 688           }
 689         }
 690       }
 691       else
 692       {
 693         // just use the id/seq set
 694         seqstr = idandseqs[1];
 695         ids = idandseqs[0];
 696         usingNames = true;
 697       }
 698       // and try and make the groupURL!
 699
 700       Object[] urlset = null;
 701       try
 702       {
 703         urlset = urlLink.makeUrlStubs(ids, seqstr,
 704                 "FromJalview" + System.currentTimeMillis(), false);
 705       } catch (UrlStringTooLongException e)
 706       {
 707       }
 708       if (urlset != null)
 709       {
 710         int type = urlLink.getGroupURLType() & 3;
 711         // System.out.println(urlLink.getGroupURLType()
 712         // +" "+((String[])urlset[3])[0]);
 713         // first two bits ofurlLink type bitfield are sequenceids and sequences
 714         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 715         addshowLink(linkMenus[type], label
 716                 + (((type & 1) == 1) ? ("("
 717                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 718                 urlLink, urlset);
 719         addMenu = true;
 720       }
 721     }
 722     if (addMenu)
 723     {
 724       groupLinksMenu = new JMenu("Group Links");
 725       for (int m = 0; m < linkMenus.length; m++)
 726       {
 727         if (linkMenus[m] != null
 728                 && linkMenus[m].getMenuComponentCount() > 0)
 729         {
 730           groupLinksMenu.add(linkMenus[m]);
 731         }
 732       }
 733
 734       groupMenu.add(groupLinksMenu);
 735     }
 736   }
 737
 738   /**
 739    * add a show URL menu item to the given linkMenu
 740    *
 741    * @param linkMenu
 742    * @param label
 743    *          - menu label string
 744    * @param url
 745    *          - url to open
 746    */
 747   private void addshowLink(JMenu linkMenu, String label, final String url)
 748   {
 749     JMenuItem item = new JMenuItem(label);
 750     item.setToolTipText("open URL: " + url);
 751     item.addActionListener(new java.awt.event.ActionListener()
 752     {
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         new Thread(new Runnable()
 756         {
 757
 758           public void run()
 759           {
 760             showLink(url);
 761           }
 762
 763         }).start();
 764       }
 765     });
 766
 767     linkMenu.add(item);
 768   }
 769
 770   /**
 771    * add a late bound groupURL item to the given linkMenu
 772    *
 773    * @param linkMenu
 774    * @param label
 775    *          - menu label string
 776    * @param urlgenerator
 777    *          GroupURLLink used to generate URL
 778    * @param urlstub
 779    *          Object array returned from the makeUrlStubs function.
 780    */
 781   private void addshowLink(JMenu linkMenu, String label,
 782           final GroupUrlLink urlgenerator, final Object[] urlstub)
 783   {
 784     JMenuItem item = new JMenuItem(label);
 785     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 786             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 787                                                                              // put
 788                                                                              // in
 789                                                                              // info
 790                                                                              // about
 791                                                                              // what
 792                                                                              // is
 793                                                                              // being
 794                                                                              // sent.
 795     item.addActionListener(new java.awt.event.ActionListener()
 796     {
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         new Thread(new Runnable()
 800         {
 801
 802           public void run()
 803           {
 804             try
 805             {
 806               showLink(urlgenerator.constructFrom(urlstub));
 807             } catch (UrlStringTooLongException e)
 808             {
 809             }
 810           }
 811
 812         }).start();
 813       }
 814     });
 815
 816     linkMenu.add(item);
 817   }
 818
 819   /**
 820    * DOCUMENT ME!
 821    *
 822    * @throws Exception
 823    *           DOCUMENT ME!
 824    */
 825   private void jbInit() throws Exception
 826   {
 827     groupMenu.setText("Group");
 828     groupMenu.setText("Selection");
 829     groupName.setText("Name");
 830     groupName.addActionListener(new java.awt.event.ActionListener()
 831     {
 832       public void actionPerformed(ActionEvent e)
 833       {
 834         groupName_actionPerformed();
 835       }
 836     });
 837     sequenceMenu.setText("Sequence");
 838     sequenceName.setText("Edit Name/Description");
 839     sequenceName.addActionListener(new java.awt.event.ActionListener()
 840     {
 841       public void actionPerformed(ActionEvent e)
 842       {
 843         sequenceName_actionPerformed();
 844       }
 845     });
 846     PIDColour.setFocusPainted(false);
 847     unGroupMenuItem.setText("Remove Group");
 848     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 849     {
 850       public void actionPerformed(ActionEvent e)
 851       {
 852         unGroupMenuItem_actionPerformed();
 853       }
 854     });
 855
 856     outline.setText("Border colour");
 857     outline.addActionListener(new java.awt.event.ActionListener()
 858     {
 859       public void actionPerformed(ActionEvent e)
 860       {
 861         outline_actionPerformed();
 862       }
 863     });
 864     nucleotideMenuItem.setText("Nucleotide");
 865     nucleotideMenuItem.addActionListener(new ActionListener()
 866     {
 867       public void actionPerformed(ActionEvent e)
 868       {
 869         nucleotideMenuItem_actionPerformed();
 870       }
 871     });
 872     colourMenu.setText("Group Colour");
 873     showBoxes.setText("Boxes");
 874     showBoxes.setState(true);
 875     showBoxes.addActionListener(new ActionListener()
 876     {
 877       public void actionPerformed(ActionEvent e)
 878       {
 879         showBoxes_actionPerformed();
 880       }
 881     });
 882     showText.setText("Text");
 883     showText.setState(true);
 884     showText.addActionListener(new ActionListener()
 885     {
 886       public void actionPerformed(ActionEvent e)
 887       {
 888         showText_actionPerformed();
 889       }
 890     });
 891     showColourText.setText("Colour Text");
 892     showColourText.addActionListener(new ActionListener()
 893     {
 894       public void actionPerformed(ActionEvent e)
 895       {
 896         showColourText_actionPerformed();
 897       }
 898     });
 899     displayNonconserved.setText("Show Nonconserved");
 900     displayNonconserved.setState(true);
 901     displayNonconserved.addActionListener(new ActionListener()
 902     {
 903       public void actionPerformed(ActionEvent e)
 904       {
 905         showNonconserved_actionPerformed();
 906       }
 907     });
 908     editMenu.setText("Edit");
 909     cut.setText("Cut");
 910     cut.addActionListener(new ActionListener()
 911     {
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         cut_actionPerformed();
 915       }
 916     });
 917     upperCase.setText("To Upper Case");
 918     upperCase.addActionListener(new ActionListener()
 919     {
 920       public void actionPerformed(ActionEvent e)
 921       {
 922         changeCase(e);
 923       }
 924     });
 925     copy.setText("Copy");
 926     copy.addActionListener(new ActionListener()
 927     {
 928       public void actionPerformed(ActionEvent e)
 929       {
 930         copy_actionPerformed();
 931       }
 932     });
 933     lowerCase.setText("To Lower Case");
 934     lowerCase.addActionListener(new ActionListener()
 935     {
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         changeCase(e);
 939       }
 940     });
 941     toggle.setText("Toggle Case");
 942     toggle.addActionListener(new ActionListener()
 943     {
 944       public void actionPerformed(ActionEvent e)
 945       {
 946         changeCase(e);
 947       }
 948     });
 949     pdbMenu.setText("Associate Structure with Sequence");
 950     pdbFromFile.setText("From File");
 951     pdbFromFile.addActionListener(new ActionListener()
 952     {
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         pdbFromFile_actionPerformed();
 956       }
 957     });
 958     enterPDB.setText("Enter PDB Id");
 959     enterPDB.addActionListener(new ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         enterPDB_actionPerformed();
 964       }
 965     });
 966     discoverPDB.setText("Discover PDB ids");
 967     discoverPDB.addActionListener(new ActionListener()
 968     {
 969       public void actionPerformed(ActionEvent e)
 970       {
 971         discoverPDB_actionPerformed();
 972       }
 973     });
 974     outputMenu.setText("Output to Textbox...");
 975     sequenceFeature.setText("Create Sequence Feature");
 976     sequenceFeature.addActionListener(new ActionListener()
 977     {
 978       public void actionPerformed(ActionEvent e)
 979       {
 980         sequenceFeature_actionPerformed();
 981       }
 982     });
 983     textColour.setText("Text Colour");
 984     textColour.addActionListener(new ActionListener()
 985     {
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         textColour_actionPerformed();
 989       }
 990     });
 991     jMenu1.setText("Group");
 992     structureMenu.setText("Structure");
 993     viewStructureMenu.setText("View Structure");
 994     // colStructureMenu.setText("Colour By Structure");
 995     editSequence.setText("Edit Sequence...");
 996     editSequence.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent actionEvent)
 999       {
1000         editSequence_actionPerformed(actionEvent);
1001       }
1002     });
1003     /*
1004      * annotationMenuItem.setText("By Annotation");
1005      * annotationMenuItem.addActionListener(new ActionListener() { public void
1006      * actionPerformed(ActionEvent actionEvent) {
1007      * annotationMenuItem_actionPerformed(actionEvent); } });
1008      */
1009
1010     add(groupMenu);
1011
1012     add(sequenceMenu);
1013     this.add(structureMenu);
1014     groupMenu.add(editMenu);
1015     groupMenu.add(outputMenu);
1016     groupMenu.add(sequenceFeature);
1017     groupMenu.add(jMenu1);
1018     sequenceMenu.add(sequenceName);
1019     colourMenu.add(textColour);
1020     colourMenu.add(noColourmenuItem);
1021     colourMenu.add(clustalColour);
1022     colourMenu.add(BLOSUM62Colour);
1023     colourMenu.add(PIDColour);
1024     colourMenu.add(zappoColour);
1025     colourMenu.add(taylorColour);
1026     colourMenu.add(hydrophobicityColour);
1027     colourMenu.add(helixColour);
1028     colourMenu.add(strandColour);
1029     colourMenu.add(turnColour);
1030     colourMenu.add(buriedColour);
1031     colourMenu.add(nucleotideMenuItem);
1032     colourMenu.add(purinePyrimidineColour);
1033     //colourMenu.add(covariationColour);
1034     colourMenu.add(userDefinedColour);
1035
1036     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1037     {
1038       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1039               .getUserColourSchemes().keys();
1040
1041       while (userColours.hasMoreElements())
1042       {
1043         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1044         item.addActionListener(new ActionListener()
1045         {
1046           public void actionPerformed(ActionEvent evt)
1047           {
1048             userDefinedColour_actionPerformed(evt);
1049           }
1050         });
1051         colourMenu.add(item);
1052       }
1053     }
1054
1055     colourMenu.addSeparator();
1056     colourMenu.add(abovePIDColour);
1057     colourMenu.add(conservationMenuItem);
1058     // colourMenu.add(annotationMenuItem);
1059     editMenu.add(copy);
1060     editMenu.add(cut);
1061     editMenu.add(editSequence);
1062     editMenu.add(upperCase);
1063     editMenu.add(lowerCase);
1064     editMenu.add(toggle);
1065     pdbMenu.add(pdbFromFile);
1066     pdbMenu.add(enterPDB);
1067     pdbMenu.add(discoverPDB);
1068     jMenu1.add(groupName);
1069     jMenu1.add(unGroupMenuItem);
1070     jMenu1.add(colourMenu);
1071     jMenu1.add(showBoxes);
1072     jMenu1.add(showText);
1073     jMenu1.add(showColourText);
1074     jMenu1.add(outline);
1075     jMenu1.add(displayNonconserved);
1076     structureMenu.add(pdbMenu);
1077     structureMenu.add(viewStructureMenu);
1078     // structureMenu.add(colStructureMenu);
1079     noColourmenuItem.setText("None");
1080     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         noColourmenuItem_actionPerformed();
1085       }
1086     });
1087
1088     clustalColour.setText("Clustalx colours");
1089     clustalColour.addActionListener(new java.awt.event.ActionListener()
1090     {
1091       public void actionPerformed(ActionEvent e)
1092       {
1093         clustalColour_actionPerformed();
1094       }
1095     });
1096     zappoColour.setText("Zappo");
1097     zappoColour.addActionListener(new java.awt.event.ActionListener()
1098     {
1099       public void actionPerformed(ActionEvent e)
1100       {
1101         zappoColour_actionPerformed();
1102       }
1103     });
1104     taylorColour.setText("Taylor");
1105     taylorColour.addActionListener(new java.awt.event.ActionListener()
1106     {
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         taylorColour_actionPerformed();
1110       }
1111     });
1112     hydrophobicityColour.setText("Hydrophobicity");
1113     hydrophobicityColour
1114             .addActionListener(new java.awt.event.ActionListener()
1115             {
1116               public void actionPerformed(ActionEvent e)
1117               {
1118                 hydrophobicityColour_actionPerformed();
1119               }
1120             });
1121     helixColour.setText("Helix propensity");
1122     helixColour.addActionListener(new java.awt.event.ActionListener()
1123     {
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         helixColour_actionPerformed();
1127       }
1128     });
1129     strandColour.setText("Strand propensity");
1130     strandColour.addActionListener(new java.awt.event.ActionListener()
1131     {
1132       public void actionPerformed(ActionEvent e)
1133       {
1134         strandColour_actionPerformed();
1135       }
1136     });
1137     turnColour.setText("Turn propensity");
1138     turnColour.addActionListener(new java.awt.event.ActionListener()
1139     {
1140       public void actionPerformed(ActionEvent e)
1141       {
1142         turnColour_actionPerformed();
1143       }
1144     });
1145     buriedColour.setText("Buried Index");
1146     buriedColour.addActionListener(new java.awt.event.ActionListener()
1147     {
1148       public void actionPerformed(ActionEvent e)
1149       {
1150         buriedColour_actionPerformed();
1151       }
1152     });
1153     abovePIDColour.setText("Above % Identity");
1154     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1155     {
1156       public void actionPerformed(ActionEvent e)
1157       {
1158         abovePIDColour_actionPerformed();
1159       }
1160     });
1161     userDefinedColour.setText("User Defined...");
1162     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1163     {
1164       public void actionPerformed(ActionEvent e)
1165       {
1166         userDefinedColour_actionPerformed(e);
1167       }
1168     });
1169     PIDColour.setText("Percentage Identity");
1170     PIDColour.addActionListener(new java.awt.event.ActionListener()
1171     {
1172       public void actionPerformed(ActionEvent e)
1173       {
1174         PIDColour_actionPerformed();
1175       }
1176     });
1177     BLOSUM62Colour.setText("BLOSUM62");
1178     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1179     {
1180       public void actionPerformed(ActionEvent e)
1181       {
1182         BLOSUM62Colour_actionPerformed();
1183       }
1184     });
1185     purinePyrimidineColour.setText("Purine/Pyrimidine");
1186     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190           purinePyrimidineColour_actionPerformed();
1191       }
1192     });
1193    /*
1194     covariationColour.addActionListener(new java.awt.event.ActionListener()
1195     {
1196       public void actionPerformed(ActionEvent e)
1197       {
1198           covariationColour_actionPerformed();
1199       }
1200     });*/
1201
1202     conservationMenuItem.setText("Conservation");
1203     conservationMenuItem
1204             .addActionListener(new java.awt.event.ActionListener()
1205             {
1206               public void actionPerformed(ActionEvent e)
1207               {
1208                 conservationMenuItem_actionPerformed();
1209               }
1210             });
1211   }
1212
1213   protected void showNonconserved_actionPerformed()
1214   {
1215     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1216     refresh();
1217   }
1218
1219   /**
1220    * call to refresh view after settings change
1221    */
1222   void refresh()
1223   {
1224     ap.updateAnnotation();
1225     ap.paintAlignment(true);
1226
1227     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1228   }
1229
1230   /**
1231    * DOCUMENT ME!
1232    *
1233    * @param e
1234    *          DOCUMENT ME!
1235    */
1236   protected void clustalColour_actionPerformed()
1237   {
1238     SequenceGroup sg = getGroup();
1239     sg.cs = new ClustalxColourScheme(
1240             sg.getSequences(ap.av.hiddenRepSequences),
1241             ap.av.alignment.getWidth());
1242     refresh();
1243   }
1244
1245   /**
1246    * DOCUMENT ME!
1247    *
1248    * @param e
1249    *          DOCUMENT ME!
1250    */
1251   protected void zappoColour_actionPerformed()
1252   {
1253     getGroup().cs = new ZappoColourScheme();
1254     refresh();
1255   }
1256
1257   /**
1258    * DOCUMENT ME!
1259    *
1260    * @param e
1261    *          DOCUMENT ME!
1262    */
1263   protected void taylorColour_actionPerformed()
1264   {
1265     getGroup().cs = new TaylorColourScheme();
1266     refresh();
1267   }
1268
1269   /**
1270    * DOCUMENT ME!
1271    *
1272    * @param e
1273    *          DOCUMENT ME!
1274    */
1275   protected void hydrophobicityColour_actionPerformed()
1276   {
1277     getGroup().cs = new HydrophobicColourScheme();
1278     refresh();
1279   }
1280
1281   /**
1282    * DOCUMENT ME!
1283    *
1284    * @param e
1285    *          DOCUMENT ME!
1286    */
1287   protected void helixColour_actionPerformed()
1288   {
1289     getGroup().cs = new HelixColourScheme();
1290     refresh();
1291   }
1292
1293   /**
1294    * DOCUMENT ME!
1295    *
1296    * @param e
1297    *          DOCUMENT ME!
1298    */
1299   protected void strandColour_actionPerformed()
1300   {
1301     getGroup().cs = new StrandColourScheme();
1302     refresh();
1303   }
1304
1305   /**
1306    * DOCUMENT ME!
1307    *
1308    * @param e
1309    *          DOCUMENT ME!
1310    */
1311   protected void turnColour_actionPerformed()
1312   {
1313     getGroup().cs = new TurnColourScheme();
1314     refresh();
1315   }
1316
1317   /**
1318    * DOCUMENT ME!
1319    *
1320    * @param e
1321    *          DOCUMENT ME!
1322    */
1323   protected void buriedColour_actionPerformed()
1324   {
1325     getGroup().cs = new BuriedColourScheme();
1326     refresh();
1327   }
1328
1329   /**
1330    * DOCUMENT ME!
1331    *
1332    * @param e
1333    *          DOCUMENT ME!
1334    */
1335   public void nucleotideMenuItem_actionPerformed()
1336   {
1337     getGroup().cs = new NucleotideColourScheme();
1338     refresh();
1339   }
1340
1341   protected void purinePyrimidineColour_actionPerformed()
1342   {
1343     getGroup().cs = new PurinePyrimidineColourScheme();
1344     refresh();
1345   }
1346   /*
1347   protected void covariationColour_actionPerformed()
1348   {
1349     getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
1350     refresh();
1351   }
1352 */
1353   /**
1354    * DOCUMENT ME!
1355    *
1356    * @param e
1357    *          DOCUMENT ME!
1358    */
1359   protected void abovePIDColour_actionPerformed()
1360   {
1361     SequenceGroup sg = getGroup();
1362     if (sg.cs == null)
1363     {
1364       return;
1365     }
1366
1367     if (abovePIDColour.isSelected())
1368     {
1369       sg.cs.setConsensus(AAFrequency.calculate(
1370               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1371               sg.getEndRes() + 1));
1372
1373       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1374               .getName());
1375
1376       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1377
1378       SliderPanel.showPIDSlider();
1379     }
1380     else
1381     // remove PIDColouring
1382     {
1383       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1384     }
1385
1386     refresh();
1387   }
1388
1389   /**
1390    * DOCUMENT ME!
1391    *
1392    * @param e
1393    *          DOCUMENT ME!
1394    */
1395   protected void userDefinedColour_actionPerformed(ActionEvent e)
1396   {
1397     SequenceGroup sg = getGroup();
1398
1399     if (e.getActionCommand().equals("User Defined..."))
1400     {
1401       new UserDefinedColours(ap, sg);
1402     }
1403     else
1404     {
1405       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1406               .getUserColourSchemes().get(e.getActionCommand());
1407
1408       sg.cs = udc;
1409     }
1410     refresh();
1411   }
1412
1413   /**
1414    * DOCUMENT ME!
1415    *
1416    * @param e
1417    *          DOCUMENT ME!
1418    */
1419   protected void PIDColour_actionPerformed()
1420   {
1421     SequenceGroup sg = getGroup();
1422     sg.cs = new PIDColourScheme();
1423     sg.cs.setConsensus(AAFrequency.calculate(
1424             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1425             sg.getEndRes() + 1));
1426     refresh();
1427   }
1428
1429   /**
1430    * DOCUMENT ME!
1431    *
1432    * @param e
1433    *          DOCUMENT ME!
1434    */
1435   protected void BLOSUM62Colour_actionPerformed()
1436   {
1437     SequenceGroup sg = getGroup();
1438
1439     sg.cs = new Blosum62ColourScheme();
1440
1441     sg.cs.setConsensus(AAFrequency.calculate(
1442             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1443             sg.getEndRes() + 1));
1444
1445     refresh();
1446   }
1447
1448   /**
1449    * DOCUMENT ME!
1450    *
1451    * @param e
1452    *          DOCUMENT ME!
1453    */
1454   protected void noColourmenuItem_actionPerformed()
1455   {
1456     getGroup().cs = null;
1457     refresh();
1458   }
1459
1460   /**
1461    * DOCUMENT ME!
1462    *
1463    * @param e
1464    *          DOCUMENT ME!
1465    */
1466   protected void conservationMenuItem_actionPerformed()
1467   {
1468     SequenceGroup sg = getGroup();
1469     if (sg.cs == null)
1470     {
1471       return;
1472     }
1473
1474     if (conservationMenuItem.isSelected())
1475     {
1476       Conservation c = new Conservation("Group",
1477               ResidueProperties.propHash, 3,
1478               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1479               sg.getEndRes() + 1);
1480
1481       c.calculate();
1482       c.verdict(false, ap.av.ConsPercGaps);
1483
1484       sg.cs.setConservation(c);
1485
1486       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1487       SliderPanel.showConservationSlider();
1488     }
1489     else
1490     // remove ConservationColouring
1491     {
1492       sg.cs.setConservation(null);
1493     }
1494
1495     refresh();
1496   }
1497
1498   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1499   {
1500     SequenceGroup sg = getGroup();
1501     if (sg == null)
1502     {
1503       return;
1504     }
1505
1506     AnnotationColourGradient acg = new AnnotationColourGradient(
1507             sequence.getAnnotation()[0], null,
1508             AnnotationColourGradient.NO_THRESHOLD);
1509
1510     acg.predefinedColours = true;
1511     sg.cs = acg;
1512
1513     refresh();
1514   }
1515
1516   /**
1517    * DOCUMENT ME!
1518    *
1519    * @param e
1520    *          DOCUMENT ME!
1521    */
1522   protected void groupName_actionPerformed()
1523   {
1524
1525     SequenceGroup sg = getGroup();
1526     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1527             sg.getDescription(), "       Group Name ",
1528             "Group Description ", "Edit Group Name/Description",
1529             ap.alignFrame);
1530
1531     if (!dialog.accept)
1532     {
1533       return;
1534     }
1535
1536     sg.setName(dialog.getName());
1537     sg.setDescription(dialog.getDescription());
1538     refresh();
1539   }
1540
1541   /**
1542    * Get selection group - adding it to the alignment if necessary.
1543    *
1544    * @return sequence group to operate on
1545    */
1546   SequenceGroup getGroup()
1547   {
1548     SequenceGroup sg = ap.av.getSelectionGroup();
1549     // this method won't add a new group if it already exists
1550     if (sg != null)
1551     {
1552       ap.av.alignment.addGroup(sg);
1553     }
1554
1555     return sg;
1556   }
1557
1558   /**
1559    * DOCUMENT ME!
1560    *
1561    * @param e
1562    *          DOCUMENT ME!
1563    */
1564   void sequenceName_actionPerformed()
1565   {
1566     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1567             sequence.getDescription(), "       Sequence Name ",
1568             "Sequence Description ", "Edit Sequence Name/Description",
1569             ap.alignFrame);
1570
1571     if (!dialog.accept)
1572     {
1573       return;
1574     }
1575
1576     if (dialog.getName() != null)
1577     {
1578       if (dialog.getName().indexOf(" ") > -1)
1579       {
1580         JOptionPane.showMessageDialog(ap,
1581                 "Spaces have been converted to \"_\"",
1582                 "No spaces allowed in Sequence Name",
1583                 JOptionPane.WARNING_MESSAGE);
1584       }
1585
1586       sequence.setName(dialog.getName().replace(' ', '_'));
1587       ap.paintAlignment(false);
1588     }
1589
1590     sequence.setDescription(dialog.getDescription());
1591
1592     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1593             .getSequences());
1594
1595   }
1596
1597   /**
1598    * DOCUMENT ME!
1599    *
1600    * @param e
1601    *          DOCUMENT ME!
1602    */
1603   void unGroupMenuItem_actionPerformed()
1604   {
1605     SequenceGroup sg = ap.av.getSelectionGroup();
1606     ap.av.alignment.deleteGroup(sg);
1607     ap.av.setSelectionGroup(null);
1608     refresh();
1609   }
1610
1611   /**
1612    * DOCUMENT ME!
1613    *
1614    * @param e
1615    *          DOCUMENT ME!
1616    */
1617   protected void outline_actionPerformed()
1618   {
1619     SequenceGroup sg = getGroup();
1620     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1621             Color.BLUE);
1622
1623     if (col != null)
1624     {
1625       sg.setOutlineColour(col);
1626     }
1627
1628     refresh();
1629   }
1630
1631   /**
1632    * DOCUMENT ME!
1633    *
1634    * @param e
1635    *          DOCUMENT ME!
1636    */
1637   public void showBoxes_actionPerformed()
1638   {
1639     getGroup().setDisplayBoxes(showBoxes.isSelected());
1640     refresh();
1641   }
1642
1643   /**
1644    * DOCUMENT ME!
1645    *
1646    * @param e
1647    *          DOCUMENT ME!
1648    */
1649   public void showText_actionPerformed()
1650   {
1651     getGroup().setDisplayText(showText.isSelected());
1652     refresh();
1653   }
1654
1655   /**
1656    * DOCUMENT ME!
1657    *
1658    * @param e
1659    *          DOCUMENT ME!
1660    */
1661   public void showColourText_actionPerformed()
1662   {
1663     getGroup().setColourText(showColourText.isSelected());
1664     refresh();
1665   }
1666
1667   public void showLink(String url)
1668   {
1669     try
1670     {
1671       jalview.util.BrowserLauncher.openURL(url);
1672     } catch (Exception ex)
1673     {
1674       JOptionPane
1675               .showInternalMessageDialog(
1676                       Desktop.desktop,
1677                       "Unixers: Couldn't find default web browser."
1678                               + "\nAdd the full path to your browser in Preferences.",
1679                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1680
1681       ex.printStackTrace();
1682     }
1683   }
1684
1685   void hideSequences(boolean representGroup)
1686   {
1687     SequenceGroup sg = ap.av.getSelectionGroup();
1688     if (sg == null || sg.getSize() < 1)
1689     {
1690       ap.av.hideSequence(new SequenceI[]
1691       { sequence });
1692       return;
1693     }
1694
1695     ap.av.setSelectionGroup(null);
1696
1697     if (representGroup)
1698     {
1699       ap.av.hideRepSequences(sequence, sg);
1700
1701       return;
1702     }
1703
1704     int gsize = sg.getSize();
1705     SequenceI[] hseqs;
1706
1707     hseqs = new SequenceI[gsize];
1708
1709     int index = 0;
1710     for (int i = 0; i < gsize; i++)
1711     {
1712       hseqs[index++] = sg.getSequenceAt(i);
1713     }
1714
1715     ap.av.hideSequence(hseqs);
1716     // refresh(); TODO: ? needed ?
1717     ap.av.sendSelection();
1718   }
1719
1720   public void copy_actionPerformed()
1721   {
1722     ap.alignFrame.copy_actionPerformed(null);
1723   }
1724
1725   public void cut_actionPerformed()
1726   {
1727     ap.alignFrame.cut_actionPerformed(null);
1728   }
1729
1730   void changeCase(ActionEvent e)
1731   {
1732     Object source = e.getSource();
1733     SequenceGroup sg = ap.av.getSelectionGroup();
1734
1735     if (sg != null)
1736     {
1737       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1738               sg.getEndRes() + 1);
1739
1740       String description;
1741       int caseChange;
1742
1743       if (source == toggle)
1744       {
1745         description = "Toggle Case";
1746         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1747       }
1748       else if (source == upperCase)
1749       {
1750         description = "To Upper Case";
1751         caseChange = ChangeCaseCommand.TO_UPPER;
1752       }
1753       else
1754       {
1755         description = "To Lower Case";
1756         caseChange = ChangeCaseCommand.TO_LOWER;
1757       }
1758
1759       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1760               sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1761               caseChange);
1762
1763       ap.alignFrame.addHistoryItem(caseCommand);
1764
1765       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1766               .getSequences());
1767
1768     }
1769   }
1770
1771   public void outputText_actionPerformed(ActionEvent e)
1772   {
1773     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1774     cap.setForInput(null);
1775     Desktop.addInternalFrame(cap,
1776             "Alignment output - " + e.getActionCommand(), 600, 500);
1777
1778     String[] omitHidden = null;
1779
1780     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1781     // or we simply trust the user wants
1782     // wysiwig behaviour
1783     SequenceGroup sg = ap.av.getSelectionGroup();
1784     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1785     omitHidden = ap.av.getViewAsString(true);
1786     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1787     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1788     if (nala != null)
1789     {
1790       for (int i = 0; i < nala.length; i++)
1791       {
1792         AlignmentAnnotation na = nala[i];
1793         oal.addAnnotation(na);
1794       }
1795     }
1796     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1797             oal, omitHidden, csel, sg));
1798     oal = null;
1799   }
1800
1801   public void pdbFromFile_actionPerformed()
1802   {
1803     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1804             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1805     chooser.setFileView(new jalview.io.JalviewFileView());
1806     chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1807     chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1808
1809     int value = chooser.showOpenDialog(null);
1810
1811     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1812     {
1813       String choice = chooser.getSelectedFile().getPath();
1814       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1815       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1816     }
1817
1818   }
1819
1820   public void enterPDB_actionPerformed()
1821   {
1822     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1823             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1824
1825     if (id != null && id.length() > 0)
1826     {
1827       PDBEntry entry = new PDBEntry();
1828       entry.setId(id.toUpperCase());
1829       sequence.getDatasetSequence().addPDBId(entry);
1830     }
1831   }
1832
1833   public void discoverPDB_actionPerformed()
1834   {
1835
1836     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1837     { sequence }
1838             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1839     Thread discpdb = new Thread(new Runnable()
1840     {
1841       public void run()
1842       {
1843
1844         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1845                 .fetchDBRefs(false);
1846       }
1847
1848     });
1849     discpdb.start();
1850   }
1851
1852   public void sequenceFeature_actionPerformed()
1853   {
1854     SequenceGroup sg = ap.av.getSelectionGroup();
1855     if (sg == null)
1856     {
1857       return;
1858     }
1859
1860     int rsize = 0, gSize = sg.getSize();
1861     SequenceI[] rseqs, seqs = new SequenceI[gSize];
1862     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1863
1864     for (int i = 0; i < gSize; i++)
1865     {
1866       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1867       int end = sg.findEndRes(sg.getSequenceAt(i));
1868       if (start <= end)
1869       {
1870         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1871         features[rsize] = new SequenceFeature(null, null, null, start, end,
1872                 "Jalview");
1873         rsize++;
1874       }
1875     }
1876     rseqs = new SequenceI[rsize];
1877     tfeatures = new SequenceFeature[rsize];
1878     System.arraycopy(seqs, 0, rseqs, 0, rsize);
1879     System.arraycopy(features, 0, tfeatures, 0, rsize);
1880     features = tfeatures;
1881     seqs = rseqs;
1882     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1883             features, true, ap))
1884     {
1885       ap.alignFrame.setShowSeqFeatures(true);
1886       ap.highlightSearchResults(null);
1887     }
1888   }
1889
1890   public void textColour_actionPerformed()
1891   {
1892     SequenceGroup sg = getGroup();
1893     if (sg != null)
1894     {
1895       new TextColourChooser().chooseColour(ap, sg);
1896     }
1897   }
1898
1899   public void colourByStructure(String pdbid)
1900   {
1901     Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
1902                     sequence, pdbid);
1903
1904     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1905             "Coloured by " + pdbid, anots);
1906
1907     ap.av.alignment.addAnnotation(an);
1908     an.createSequenceMapping(sequence, 0, true);
1909     // an.adjustForAlignment();
1910     ap.av.alignment.setAnnotationIndex(an, 0);
1911
1912     ap.adjustAnnotationHeight();
1913
1914     sequence.addAlignmentAnnotation(an);
1915
1916   }
1917
1918   public void editSequence_actionPerformed(ActionEvent actionEvent)
1919   {
1920     SequenceGroup sg = ap.av.getSelectionGroup();
1921
1922     if (sg != null)
1923     {
1924       if (sequence == null)
1925         sequence = (Sequence) sg.getSequenceAt(0);
1926
1927       EditNameDialog dialog = new EditNameDialog(
1928               sequence.getSequenceAsString(sg.getStartRes(),
1929                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
1930               "Edit Sequence", ap.alignFrame);
1931
1932       if (dialog.accept)
1933       {
1934         EditCommand editCommand = new EditCommand("Edit Sequences",
1935                 EditCommand.REPLACE, dialog.getName().replace(' ',
1936                         ap.av.getGapCharacter()),
1937                 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1938                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1939
1940         ap.alignFrame.addHistoryItem(editCommand);
1941
1942         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1943                 .getSequences());
1944       }
1945     }
1946   }
1947
1948 }